6W73 | pdb_00006w73

Fab Structure of CD4 Binding Site (CD4bs) Huamn Monoclonal Antibody HmAb64

• PDB DOI: https://doi.org/10.2210/pdb6W73/pdb

• Classification: IMMUNE SYSTEM
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2020-03-18 Released: 2021-03-24 
• Deposition Author(s): Kong, X., Pan, R.
• Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free: 
  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

A CD4 Binding Site (CD4bs) Monoclonal Antibody Elicited from A Human Volunteer Immunized by a DNA Prime/Protein Boost gp120 HIV Vaccine

Kong, X., Pan, R.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 47.46 kDa 
• Atom Count: 3,342 
• Modeled Residue Count: 435 
• Deposited Residue Count: 438 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HmAb64 fab light chain	A [auth L]	214	Homo sapiens	Mutation(s): 0

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
HmAb64 fab heavy chain	B [auth H]	224	Homo sapiens	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	C [auth L], D [auth L]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.263 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.178 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 91.79	α = 90
b = 59.352	β = 96.215
c = 75.571	γ = 90

Software Package:

Software Name	Purpose
XDS	data processing
XDS	data scaling
XDS	data reduction
PHENIX	phasing
PHENIX	refinement

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-03-24 
Deposition Author(s): Kong, X., Pan, R.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI100151
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)	United States	AI145655

Revision History  

• Version 1.0: 2021-03-24
  Type: Initial release
  
• Version 1.1: 2023-10-18
  Changes: Advisory, Data collection, Database references, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary